Down syndrome (DS) is one of the strongest risk factors for both congenital heart disease (CHD) and acute leukemia. For instance, children with DS have a 2000-fold increased risk of atrioventricular septal defects (AVSD) and a 20-fold increased risk of acute lymphoblastic leukemia (ALL). This is especially notable since DS has a birth prevalence of 1 in 691, which has been steadily increasing in recent decades, making it one of the most common genetic syndromes. Although these increased risks have been recognized for over 50 years, the biological factors underlying these associations remain unknown. While increased dosage of genes on chromosome 21 likely contributes to this risk, trisomy 21 is not sufficient by itself to cause these phenotypes, as AVSD occurs in only 20% of individuals and the lifetime risk of ALL among children with DS is only 2%. Recently, it has been hypothesized that having an extra copy of chromosome 21 may ?move? the susceptibility threshold for disease in these children with genetic variants at other loci specifically contributing to predisposition to each disease. There is also growing interest in the disrupted developmental pathways that may lead both to structural birth defects and childhood cancer. In response to this, we have assembled a multi-disciplinary team of investigators to characterize CHD and ALL risk in children with DS. Collectively, we bring extensive experience in the genetic epidemiology of structural birth defects and childhood cancer (Dr. Philip Lupo); the risk of CHD among children with DS (Dr. Stephanie Sherman); the etiology and genomics of DS-ALL (Dr. Karen Rabin); and germline and somatic genomics of ALL (Dr. Jun Yang). In fact, we have already led: 1) the first genome-wide association study (GWAS) of DS-AVSD, which suggested common genetic variation does not explain the increased risk of AVSD among those with DS; 2) the first GWAS of DS-ALL, which indicated that loci in ALL susceptibility genes (e.g., CDKN2A, IKZF1) have stronger effects in children with DS-ALL compared to non-DS-ALL; and 3) molecular studies of DS-ALL, which demonstrated that DS-ALL exhibits distinctive immunophenotypic and cytogenetic characteristics compared to non-DS-ALL, including a 10-fold increased frequency of somatic alterations of the JAK pathway. This work suggests a unique CHD and ALL susceptibility pattern in the background of trisomy 21 that contributes to disease risk in this population. Importantly, this was accomplished through collaboration and data sharing across groups. In fact, through our combined efforts, we have assembled one of the largest DS cohorts, with over 4,000 unique samples, which include: ? DS-ALL paired germline and leukemia samples: N=444 germline; N=408 paired leukemic samples ? DS-CHD samples: N=1,389 probands; N=877 parents ? DS ?alone? samples: N=992 probands; N=409 parents (includes phenotype data from medical records and questionnaires) An important component of the INCLUDE Project is to generate a ?molecular snapshot of DS through a cohort study.? To this end, we are requesting that ~2,000 of the samples included in our DS cohort be included for whole-genome sequencing (WGS) as part of the INCLUDE Project. As described in our original Gabriella Miller Kids First application, the overarching goals of our project are to: 1) identify genetic variants underlying AVSD in children with DS, and 2) identify genetic variants underlying ALL in children with DS. Based on the goals of the Kids First Program, we recognize that the DS-ALL and DS-CHD samples would be prioritized for WGS. However, we propose that additional WGS of this cohort could be leveraged for: 1) understanding the genetic background of children with DS that do not develop CHD or ALL, 2) exploring the role of de novo mutations in CHD and ALL susceptibility through the inclusion of parental samples; and 3) investigating the genetics of other outcomes in children with DS. Therefore, we propose to capitalize on various related NIH initiatives (e.g., Kids First, INCLUDE, and TOPMed) to complete genomic profiling of this unique DS cohort in its entirety, with careful coordination and integration amongst different programs. To this end, we are requesting support from INCLUDE to augment the number of samples that can be sequenced from the combined cohort described in our Kids First and TOPMed X01 proposals. To complement this, we are requesting a separate INCLUDE supplement focusing on ALL led by Drs. Rabin, Yang, and Lupo for 1) deep phenotyping of DS-ALL; 2) establishing patient-derived xenograft models; and 3) performing ALL transcriptomics and epigenomics. If this series of requests is funded, this cohort with deep phenotyping (enriched for those who develop CHD and ALL) and pan-omics data could be leveraged to generate a wealth of new insights into the molecular mechanisms underlying disease risk in those with DS for years to come. Additionally, we welcome the opportunity to collaborate with Kids First, TOPMed, and INCLUDE program staff to select the samples that would be of highest programmatic priority and scientific value.